Infectious Disease Roundup: 1/27/2025

Influenza A In Focus: A new highly pathogenic bird flu has dropped and the UK reports its first human case of H5N1.

Special Note: The United States Health and Human Services is still under a communications embargo that has also impacted some of their agencies’ abilities to order supplies. This can directly impact ongoing experiments and clinical trials. I encourage my readers to both call and write to their congressional representatives regarding the importance of HHS operations. The list of these agencies and their activities can be found here.

During my research for this post I noticed a broken CDC link regarding avian influenza. As I do not know if this page was simply moved or not, I am flagging this finding as something that is atypical. Links from the WHO website to the CDC are typically carefully maintained.

The broken link pointed to this information which no longer appears to be available on the CDC website:

Here is the URL for the page where information is no longer available: https://www.cdc.gov/flu/avianflu/spotlights/2023-2024/h5n1-analysis-texas.htm

Influenza A Introduction

Influenza A is a deadly virus. In a bad ‘flu season’ in the United States up to 60,000 may die and over 700,000 may be infected. Influenza infection can cause life-long complications, though this is more rare than SARS-CoV-2 causing Long-COVID. Influenza vaccines are not typically as effective in prevention of viral infection as other vaccines, but they do significantly reduce severity of disease, hospitalization, and death. We are nearing what will likely be the peak of the influenza season in the northern hemisphere, though it may be prolonged well into February or March due to persistent cold temperatures across the United States and Europe.

First Case of H5N1 in a Person in The United Kingdom

Today, the United Kingdom reported it’s first detected human case of H5N1. The infected person had extensive exposure to poultry on a farm. For those of you tracking genotypes of H5N1, this one is the DI.2 genotype, which is both rare and distinct from the variants in clade 2.3.4.4b circulating in wild bird populations in the United States. The patient has been reported as “well” though they were admitted to the hospital, possibly for observation or to reduce spread.

The CDC was able to submit it’s most recent H5N1 genotype sequencing dated 1/26/2025 to the GSAID database which has published the lineages, showing that there are several new mutations. New lineages have been found in everything from cow milk to raw pet food, and have been reported in multiple US states (see images below). Note, based on all of the science I do not think there is any danger of influenza infection from pasteurized milk or cooked egg consumption.

As of January 17th, 2025, the CDC reported that 136 million birds have been affected by clade 2.3.4.4 H5N1 across 51 states, 606 counties in 1,420 outbreaks. This is data from 10 days ago and since then new outbreaks have been reported at the local level across the northeastern United States. A total of 943 dairy herd outbreaks of H5N1 have been reported. 726 of the dairy herd outbreaks have been in California, the largest milk producing state in the United States.

First Detection of Highly Pathogenic H5N9 in the United States

Today in California the first detection of H5N9 in the United states was reported at a poultry farm in Merced County, about 130 miles east of the city of San Francisco. H5N9 is also considered a highly pathogenic version of avian influenza and likely comes from a reassortment (recombination) of H5N1, H7N9, and H9N2. It was first isolated and sequenced in 2015.

More can be read about the virus in this first publication on it: Newly Emergent Highly Pathogenic H5N9 Subtype Avian Influenza A Virus, Yu Y. et al. Journal of Virology, 2015

What is particularly concerning about H5N9 is that while H5N1 is also highly pathogenic, the global human population has some pre-existing immunity through infection by or vaccination for H1N1 (the dominant Influenza A strain) where the N1 in both viruses has been shown to provide protection from severe disease (please see my prior write up on H5N1 for more details: here). Although no human cases have been reported for H5N9, H7N9 the highly pathogenic influenza strain where the N9 came from is capable of infecting humans and is considered highly pathogenic.

Let’s run that back. We have the H5 of a highly pathogenic human infecting virus combined with the N9 of a highly pathogenic human infecting virus to create H5N9. If I were a betting person, I’d bet on H5N9 being highly pathogenic in humans.

Also, because the human population does not currently have pre-existing immunity to H5N9 (or H5N7) meaning that an outbreak of this virus could be even more devastating that what has been anticipated with an H5N1 outbreak.

H5N9 has until now been considered rare, and is still listed as such in web searches. Finding it among a commercial bird flock in California indicates that H5N9 may not be as rare as we thought.

Note: If this is concerning to you (it is for me) please urge your congressional representatives to allow for the US Human Health Services, which includes the CDC (that has task forces that can identify, isolate, and contain novel viral spread) to resume normal activities. Also consider that we will likely need new vaccines to effectively protect our population, pets, and livestock from these emerging highly pathogenic influenza strains.

Another Note of Caution on H5N1

One ingredient necessary for a virus to become pandemic causing is how hearty it is (how long it lives) and how well it spreads (how easily it infects someone). These two virus traits as you might image are linked in real life. For example, the longer a virus can live on a surface, the more opportunities it has to infect someone.

In my research on H5N1 traits I found a CDC publication from 2022 that details the resiliency of H5N1. Linked here: “Higher Viral Stability and Ethanol Resistance of Avian Influenza A(H5N1) Virus on Human Skin” H5N1 is indeed less susceptible to alcohol based hand sanitizers and can live longer on surfaces and skin than a typical influenza A virus.

Hand sanitizer is certainly better than nothing, but if you have the opportunity to wash your hands with soap and warm water, that may be better at reducing potential infection.